Original article

A peek into the microbiome of two free-living aquatic nematodes – Anticoma & Daptonema

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Abstract:

Despite the fact that nematodes and bacteria are most diverse and most abundant forms of life in sediment habitats, their togetherness is never explored especially for free-living forms. To bridge this gap in knowledge, we studied two numerically dominant nematode species, Anticoma litoris and Damptonema sp. at Oregon Inlet, NC, and explored their microbial community profiles using the marker 16S rRNA subunit gene. We primarily used multiple displacement amplification (MDA) followed by PCR, denaturing gradient gel electrophoresis (DGGE), amplification and sequenced bands to identify microbial taxa. We also cultivated bacterial taxa after cultivating from squashed individual nematodes. Our findings using culture method showed the microbiome of both nematode taxa to be dominated by Bacilli and Gammaproteobacteria, but results of the MDA-DGGE-PCR method showed a much greater diversity and revealed several exclusive associations. Microbial community profiles of the two nematodes differed greatly among the two species and from the overall sediment bacterial profile, indicating possible selectivity by nematodes in their bacterial associations and specialization in their ecological niche.

HIGHLIGHTS

  • We used multiple displacement amplification (MDA) of entire microbial community DNA followed by PCR and denaturing gradient gel electrophoresis (DGGE) to elucidate microbiome of Anticoma litoris and Daptonema sp.
  • MDA-PCR-DGGE was superior in identifying nematode bacterial associates, but failed to identify 3 genera isolated from squash plating.
  • Primer mismatch was shown to contribute to bias in molecular methods.
  • Nematode microbiome profiles were distinct and not representative of sediment environmental microbial community.
  • Microbiome profile of Daptonema sp. and A. litoris showed specificity and may represent individual taxon’s distinct ecological niche.

Keywords:

Nematode-bacterial associations, DGGE, MDA, marine nematodes


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